Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008485.1 Corchorus capsularis cultivar CVL-1 contig08506, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45026
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:109 original size:2 final size:2
Alignment explanation
Indices: 102--135 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
92 CCTCCGCTAC
102 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
136 TTGGGCACAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1089 original size:3 final size:3
Alignment explanation
Indices: 1081--1112 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1071 AAAGAAAGGG
1081 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1113 GTAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:10546 original size:2 final size:2
Alignment explanation
Indices: 10541--10569 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10531 TTCAACTATC
10541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10570 GTTCTTGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14320 original size:6 final size:6
Alignment explanation
Indices: 14309--14344 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
14299 AAGGCAGTAT
14309 TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG
1 TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG
14345 GTGAGGGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (6 bp):
TTTTGG
Found at i:15123 original size:7 final size:7
Alignment explanation
Indices: 15113--15137 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
15103 CAATCTCCCT
15113 CTTCTCA
1 CTTCTCA
15120 CTTCTCA
1 CTTCTCA
15127 CTTCTCA
1 CTTCTCA
15134 CTTC
1 CTTC
15138 CTTCCTTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.44
Consensus pattern (7 bp):
CTTCTCA
Found at i:17646 original size:2 final size:2
Alignment explanation
Indices: 17639--17668 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17629 TATCTGATCG
17639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17669 GCGACAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18816 original size:2 final size:2
Alignment explanation
Indices: 18809--18833 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18799 AGTTAATAAT
18809 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18834 TATTATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22624 original size:14 final size:14
Alignment explanation
Indices: 22605--22631 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22595 GGCGAGGGCG
22605 ATGGAGATTGGAGA
1 ATGGAGATTGGAGA
22619 ATGGAGATTGGAG
1 ATGGAGATTGGAG
22632 GGTAGTAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.44, T:0.22
Consensus pattern (14 bp):
ATGGAGATTGGAGA
Found at i:26000 original size:65 final size:66
Alignment explanation
Indices: 25896--26027 Score: 230
Period size: 65 Copynumber: 2.0 Consensus size: 66
25886 TTTAATGTGG
* *
25896 TTTGAACATGTAATAGAGGAGATCTTCAAGTGGCTCCATGATAATA-TGTGATCTAAAGGCGGAT
1 TTTGAACATGTAATAGAGGAGATCTTCAAGTGCCTCCATGACAATATTGTGATCTAAAGGCGGAT
25960 A
66 A
*
25961 TTTGAACATGTAATATAGGAGATCTTCAAGTGCCTCCATGACAATATTGTGATCTAAAGGCGGAT
1 TTTGAACATGTAATAGAGGAGATCTTCAAGTGCCTCCATGACAATATTGTGATCTAAAGGCGGAT
26026 A
66 A
26027 T
1 T
26028 CCAGGATCGA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 43 0.68
66 20 0.32
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (66 bp):
TTTGAACATGTAATAGAGGAGATCTTCAAGTGCCTCCATGACAATATTGTGATCTAAAGGCGGAT
A
Found at i:29646 original size:7 final size:8
Alignment explanation
Indices: 29610--29649 Score: 73
Period size: 8 Copynumber: 5.1 Consensus size: 8
29600 GTAGCAAAGC
29610 AAATGGCA
1 AAATGGCA
29618 AAATGGCA
1 AAATGGCA
29626 AAATGGCA
1 AAATGGCA
29634 AAATGGC-
1 AAATGGCA
29641 AAATGGCA
1 AAATGGCA
29649 A
1 A
29650 GGGATTTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 7 0.23
8 24 0.77
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.12
Consensus pattern (8 bp):
AAATGGCA
Found at i:31861 original size:12 final size:12
Alignment explanation
Indices: 31844--31871 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
31834 AAACATCCCA
31844 AAATAAAAATAC
1 AAATAAAAATAC
31856 AAATAAAAATAC
1 AAATAAAAATAC
31868 AAAT
1 AAAT
31872 GAAGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (12 bp):
AAATAAAAATAC
Found at i:32125 original size:6 final size:6
Alignment explanation
Indices: 32114--32144 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
32104 TTCTTGGAAA
32114 CAAACT CAAACT CAAACT CAAACT CAAACT C
1 CAAACT CAAACT CAAACT CAAACT CAAACT C
32145 TCCTCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.16
Consensus pattern (6 bp):
CAAACT
Found at i:37114 original size:2 final size:2
Alignment explanation
Indices: 37107--37136 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
37097 AATTTTGATG
37107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37137 CTTCCATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40102 original size:6 final size:7
Alignment explanation
Indices: 40075--40108 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
40065 GCCTCTTTCA
40075 CTTCATT
1 CTTCATT
40082 CTTCATT
1 CTTCATT
40089 CTTCATT
1 CTTCATT
40096 C-TCATT
1 CTTCATT
40102 C-TCATT
1 CTTCATT
40108 C
1 C
40109 ATAGTTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.53
Consensus pattern (7 bp):
CTTCATT
Found at i:43297 original size:46 final size:46
Alignment explanation
Indices: 43244--43335 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
43234 TCTTTCTTGA
*
43244 ATATTTCCTTCTTACCATAAATCCCATAATTGACGCCTTAAATCAG
1 ATATTTCCTTCCTACCATAAATCCCATAATTGACGCCTTAAATCAG
*
43290 ATATTTCCTTCCTACCATAAATCCCATGATTGACGCCTTAAATCAG
1 ATATTTCCTTCCTACCATAAATCCCATAATTGACGCCTTAAATCAG
43336 TTTCATCGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.34
Consensus pattern (46 bp):
ATATTTCCTTCCTACCATAAATCCCATAATTGACGCCTTAAATCAG
Done.